Python mode for processing #1 – Science To Medicine

しばし投稿が途絶えてしまったが、この間、ベイズ統計を少し横に置いて、Rの重回帰分析やグラフィックスについて理解を深めた。今週末はPython基礎体力をつけるために、Python mode for processingに取り組んだ。

JavaとPythonの違い：
Pythonは動的に変数管理を行うため、Javaのようにいちいち変数の型を宣言しなくてもよいが、慣れないと本当に気持ち悪い。あとJavaやC言語などなどほとんどの言語は、とにかくカッコ｛｝で囲んで区切っていくが、Pythonはそのかわりに行インデントで規定する。そのため、インデントを間違えるとエラーコードを頂く。特にForループ文やIf Else文等の条件文では要注意。Javaに慣れてしまったJava脳では、Pythonは慣れないと本当にやりにくい。特にPythonの二次元配列（リストでしょうか）は、Java脳にとっては難しい。

Exporing and Explaining Data with the Processing Envirnment
「Processing による情報視覚化手法」
Let’s try to translate Java-based processing codes to Python-based codes!
Ch03-Mapping

1. Java: Step00_show_map.pde

PImage mapImage;

void setup() {
  size(640, 400);
  mapImage = loadImage("map.png");
}

void draw() {
  background(255);
  image(mapImage, 0, 0);
}

PImage mapImage;

void setup() {

size(640, 400);

mapImage = loadImage("map.png");

}

void draw() {

background(255);

image(mapImage, 0, 0);

}

次にPython: Step00_show_map_py.pyde

def setup():
    global mapImage           
    size(640, 400)
    mapImage = loadImage("map.png")
    
def draw():
    global mapImage;
    background(255)
    image(mapImage, 0, 0)

def setup():

global mapImage

size(640, 400)

mapImage = loadImage("map.png")

def draw():

global mapImage;

background(255)

image(mapImage, 0, 0)

Output:

2. Java: step01_fig1_red_dots

PImage mapImage;
Table locationTable;
int rowCount;

void setup() {
  size(640, 400);
  mapImage = loadImage("map.png");
  // Make a data table from a file that contains 
  // the coordinates of each state.
  locationTable = new Table("locations.tsv");
  // The row count will be used a lot, store it locally.
  rowCount = locationTable.getRowCount();
}

void draw() {
  background(255);
  image(mapImage, 0, 0);

  // Drawing attributes for the ellipses   
  smooth();
  fill(192, 0, 0);
  noStroke();

  // Loop through the rows of the locations file and draw the points  
  for (int row = 0; row < rowCount; row++) {
    float x = locationTable.getFloat(row, 1);  // column 1
    float y = locationTable.getFloat(row, 2);  // column 2
    ellipse(x, y, 9, 9);
  }
}

PImage mapImage;

Table locationTable;

int rowCount;

void setup() {

size(640, 400);

mapImage = loadImage("map.png");

// Make a data table from a file that contains

// the coordinates of each state.

locationTable = new Table("locations.tsv");

// The row count will be used a lot, store it locally.

rowCount = locationTable.getRowCount();

}

void draw() {

background(255);

image(mapImage, 0, 0);

// Drawing attributes for the ellipses

smooth();

fill(192, 0, 0);

noStroke();

// Loop through the rows of the locations file and draw the points

for (int row = 0; row < rowCount; row++) {

float x = locationTable.getFloat(row, 1); // column 1

float y = locationTable.getFloat(row, 2); // column 2

ellipse(x, y, 9, 9);

}

Table Class　Table.pde

class Table {
  int rowCount;
  String[][] data;
   
  Table(String filename) {
    String[] rows = loadStrings(filename);
    data = new String[rows.length][];
    
    for (int i = 0; i < rows.length; i++) {
      if (trim(rows[i]).length() == 0) {
        continue; // skip empty rows
      }
      if (rows[i].startsWith("#")) {
        continue;  // skip comment lines
      }
      
      // split the row on the tabs
      String[] pieces = split(rows[i], TAB);
      // copy to the table array
      data[rowCount] = pieces;
      rowCount++;
      
      // this could be done in one fell swoop via:
      //data[rowCount++] = split(rows[i], TAB);
    }
    // resize the 'data' array as necessary
    data = (String[][]) subset(data, 0, rowCount);
  }
    
  int getRowCount() {
    return rowCount;
  }
  
  // find a row by its name, returns -1 if no row found
  int getRowIndex(String name) {
    for (int i = 0; i < rowCount; i++) {
      if (data[i][0].equals(name)) {
        return i;
      }
    }
    println("No row named '" + name + "' was found");
    return -1;
  }
  
  String getRowName(int row) {
    return getString(row, 0);
  }

  String getString(int rowIndex, int column) {
    return data[rowIndex][column];
  }
  
  String getString(String rowName, int column) {
    return getString(getRowIndex(rowName), column);
  }
 
  int getInt(String rowName, int column) {
    return parseInt(getString(rowName, column));
  }
 
  int getInt(int rowIndex, int column) {
    return parseInt(getString(rowIndex, column));
  }
  
  float getFloat(String rowName, int column) {
    return parseFloat(getString(rowName, column));
  }
  
  float getFloat(int rowIndex, int column) {
    return parseFloat(getString(rowIndex, column));
  }
    
  void setRowName(int row, String what) {
    data[row][0] = what;
  }

  void setString(int rowIndex, int column, String what) {
    data[rowIndex][column] = what;
  }
  
  void setString(String rowName, int column, String what) {
    int rowIndex = getRowIndex(rowName);
    data[rowIndex][column] = what;
  }
  
  void setInt(int rowIndex, int column, int what) {
    data[rowIndex][column] = str(what);
  }
  
  void setInt(String rowName, int column, int what) {
    int rowIndex = getRowIndex(rowName);
    data[rowIndex][column] = str(what);
  }
  
  void setFloat(int rowIndex, int column, float what) {
    data[rowIndex][column] = str(what);
  }

  void setFloat(String rowName, int column, float what) {
    int rowIndex = getRowIndex(rowName);
    data[rowIndex][column] = str(what);
  }  
}

100

101

102

103

class Table {

int rowCount;

String[][] data;

Table(String filename) {

String[] rows = loadStrings(filename);

data = new String[rows.length][];

for (int i = 0; i < rows.length; i++) {

if (trim(rows[i]).length() == 0) {

continue; // skip empty rows

}

if (rows[i].startsWith("#")) {

continue; // skip comment lines

}

// split the row on the tabs

String[] pieces = split(rows[i], TAB);

// copy to the table array

data[rowCount] = pieces;

rowCount++;

// this could be done in one fell swoop via:

//data[rowCount++] = split(rows[i], TAB);

}

// resize the 'data' array as necessary

data = (String[][]) subset(data, 0, rowCount);

}

int getRowCount() {

return rowCount;

}

// find a row by its name, returns -1 if no row found

int getRowIndex(String name) {

for (int i = 0; i < rowCount; i++) {

if (data[i][0].equals(name)) {

return i;

}

println("No row named '" + name + "' was found");

return -1;

}

String getRowName(int row) {

return getString(row, 0);

}

String getString(int rowIndex, int column) {

return data[rowIndex][column];

}

String getString(String rowName, int column) {

return getString(getRowIndex(rowName), column);

}

int getInt(String rowName, int column) {

return parseInt(getString(rowName, column));

}

int getInt(int rowIndex, int column) {

return parseInt(getString(rowIndex, column));

}

float getFloat(String rowName, int column) {

return parseFloat(getString(rowName, column));

}

float getFloat(int rowIndex, int column) {

return parseFloat(getString(rowIndex, column));

}

void setRowName(int row, String what) {

data[row][0] = what;

}

void setString(int rowIndex, int column, String what) {

data[rowIndex][column] = what;

}

void setString(String rowName, int column, String what) {

int rowIndex = getRowIndex(rowName);

data[rowIndex][column] = what;

}

void setInt(int rowIndex, int column, int what) {

data[rowIndex][column] = str(what);

}

void setInt(String rowName, int column, int what) {

int rowIndex = getRowIndex(rowName);

data[rowIndex][column] = str(what);

}

void setFloat(int rowIndex, int column, float what) {

data[rowIndex][column] = str(what);

}

void setFloat(String rowName, int column, float what) {

int rowIndex = getRowIndex(rowName);

data[rowIndex][column] = str(what);

}

Next, Python: step01_fig1_red_dots_py.pyde

import Table

def setup():
    global locationTable
    global mapImage
    global rowCount

    size(640, 400)
    mapImage = loadImage("map.png")
    locationTable = Table.Table("locations.tsv")
    rowCount = locationTable.getRowCount()
    print rowCount
   
def draw():
    global locationTable
    global mapImage
    global rowCount
    
    background(255)

    image(mapImage, 0, 0)
    noStroke()
    fill(192, 0, 0)
    for row in range(0,rowCount):
        x = locationTable.getFloat(row, 1)
        y = locationTable.getFloat(row, 2)
        ellipse(x, y, 9, 9)

import Table

def setup():

global locationTable

global mapImage

global rowCount

size(640, 400)

mapImage = loadImage("map.png")

locationTable = Table.Table("locations.tsv")

rowCount = locationTable.getRowCount()

print rowCount

def draw():

global locationTable

global mapImage

global rowCount

background(255)

image(mapImage, 0, 0)

noStroke()

fill(192, 0, 0)

for row in range(0,rowCount):

x = locationTable.getFloat(row, 1)

y = locationTable.getFloat(row, 2)

ellipse(x, y, 9, 9)

Table Class　Table.py

class Table():
    def __init__(self, filename):
        self.filename = filename    
        self.rowCount = 0
        self.rowsTable = loadStrings(self.filename)
        self.rowIndex = 0
        self.pieces  = []
        self.data = []
        self.data2 = []
        self.value = 0
                            
        for i in range(len(self.rowsTable)):                                                                         
            if len(self.rowsTable[i].strip()) == 0:
                continue 
            if self.rowsTable[i].startswith('#'):
                continue              
            
            self.pieces = split(self.rowsTable[self.rowCount], TAB)    
            self.data = [self.pieces[i] for i in range (len(self.pieces))]   
            self.data2.append(self.data)                      
        
            self.rowCount+=1
            
    def getRowCount(self):
        return self.rowCount
    
    def getRowIndex(self, rowName):
        for i in range(self.rowCount): 
            if (self.data2[i][0] == rowName):
                return i
        return -1
    
    def getRowName(self, row):
        return self.data2[row][0]

    def getString(self, rowIndex, column):
        return self.data2[rowIndex][column]

    def getString2(self, rowName, column):
        for i in range(self.rowCount): 
            if self.data2[i][0]==rowName:
                return self.data2[i][column]
        return -1

    def getInt(self, rowIndex, column):
         return int(self.data2[rowIndex][column])

    def getInt2(self, rowName, column):
        for i in range(self.rowCount): 
            if (self.data2[i][0].equals(rowName)):
                return int(self.data2[i][column])
        return -1
    
    def getFloat(self, rowIndex, column):
        return float(self.data2[rowIndex][column])

    def getFloat2(self, rowName, column):
        for i in range(self.rowCount): 
            if (self.data2[i][0]==(rowName)):
                return float(self.data2[i][column])
        return -1
     
    def setFloat(self, rowIndex, column, what):
        self.data2[rowIndex][column] = str(what)

    def setFloat2(self, rowName, column, what):
        rowIndex = getRowIndex(self, rowName)
        self.data2[rowIndex][column] = str(what)

class Table():

def __init__(self, filename):

self.filename = filename

self.rowCount = 0

self.rowsTable = loadStrings(self.filename)

self.rowIndex = 0

self.pieces = []

self.data = []

self.data2 = []

self.value = 0

for i in range(len(self.rowsTable)):

if len(self.rowsTable[i].strip()) == 0:

continue

if self.rowsTable[i].startswith('#'):

continue

self.pieces = split(self.rowsTable[self.rowCount], TAB)

self.data = [self.pieces[i] for i in range (len(self.pieces))]

self.data2.append(self.data)

self.rowCount+=1

def getRowCount(self):

return self.rowCount

def getRowIndex(self, rowName):

for i in range(self.rowCount):

if (self.data2[i][0] == rowName):

return i

return -1

def getRowName(self, row):

return self.data2[row][0]

def getString(self, rowIndex, column):

return self.data2[rowIndex][column]

def getString2(self, rowName, column):

for i in range(self.rowCount):

if self.data2[i][0]==rowName:

return self.data2[i][column]

return -1

def getInt(self, rowIndex, column):

return int(self.data2[rowIndex][column])

def getInt2(self, rowName, column):

for i in range(self.rowCount):

if (self.data2[i][0].equals(rowName)):

return int(self.data2[i][column])

return -1

def getFloat(self, rowIndex, column):

return float(self.data2[rowIndex][column])

def getFloat2(self, rowName, column):

for i in range(self.rowCount):

if (self.data2[i][0]==(rowName)):

return float(self.data2[i][column])

return -1

def setFloat(self, rowIndex, column, what):

self.data2[rowIndex][column] = str(what)

def setFloat2(self, rowName, column, what):

rowIndex = getRowIndex(self, rowName)

self.data2[rowIndex][column] = str(what)

Output:

3. step02_fig2_varying_sizes.pde

PImage mapImage;
Table locationTable;
int rowCount;

Table dataTable;
float dataMin = MAX_FLOAT;
float dataMax = MIN_FLOAT;

void setup() {
  size(640, 400);
  mapImage = loadImage("map.png");
  locationTable = new Table("locations.tsv");
  rowCount = locationTable.getRowCount();
  
  // Read the data table
  dataTable = new Table("random.tsv");

  // Find the minimum and maximum values
  for (int row = 0; row < rowCount; row++) {
    float value = dataTable.getFloat(row, 1);
    if (value > dataMax) {
      dataMax = value;
    }
    if (value < dataMin) {
      dataMin = value;
    }
  }
}

void draw() {
  background(255);
  image(mapImage, 0, 0);
  
  smooth();
  fill(192, 0, 0);
  noStroke();
  
  for (int row = 0; row < rowCount; row++) {
    String abbrev = dataTable.getRowName(row);
    float x = locationTable.getFloat(abbrev, 1);
    float y = locationTable.getFloat(abbrev, 2);
    drawData(x, y, abbrev);
  }
}

// Map the size of the ellipse to the data value
void drawData(float x, float y, String abbrev) {
  // Get data value for state
  float value = dataTable.getFloat(abbrev, 1);
  // Re-map the value to a number between 2 and 40
  float mapped = map(value, dataMin, dataMax, 2, 40);
  // Draw an ellipse for this item
  ellipse(x, y, mapped, mapped);
}

PImage mapImage;

Table locationTable;

int rowCount;

Table dataTable;

float dataMin = MAX_FLOAT;

float dataMax = MIN_FLOAT;

void setup() {

size(640, 400);

mapImage = loadImage("map.png");

locationTable = new Table("locations.tsv");

rowCount = locationTable.getRowCount();

// Read the data table

dataTable = new Table("random.tsv");

// Find the minimum and maximum values

for (int row = 0; row < rowCount; row++) {

float value = dataTable.getFloat(row, 1);

if (value > dataMax) {

dataMax = value;

}

if (value < dataMin) {

dataMin = value;

}

void draw() {

background(255);

image(mapImage, 0, 0);

smooth();

fill(192, 0, 0);

noStroke();

for (int row = 0; row < rowCount; row++) {

String abbrev = dataTable.getRowName(row);

float x = locationTable.getFloat(abbrev, 1);

float y = locationTable.getFloat(abbrev, 2);

drawData(x, y, abbrev);

}

// Map the size of the ellipse to the data value

void drawData(float x, float y, String abbrev) {

// Get data value for state

float value = dataTable.getFloat(abbrev, 1);

// Re-map the value to a number between 2 and 40

float mapped = map(value, dataMin, dataMax, 2, 40);

// Draw an ellipse for this item

ellipse(x, y, mapped, mapped);

}

step02_fig2_varying_sizes_py.pyde

import Table

dataMin = 0
dataMax = 0

def setup():
    global locationTable
    global mapImage
    global rowCount

    global dataTable
    global dataMin
    global dataMax

    size(640, 400)
    
    mapImage = loadImage("map.png")
    locationTable = Table.Table("locations.tsv")
    rowCount = locationTable.getRowCount()
   
    dataTable = Table.Table("random.tsv")
    # Find the minimum and maximum values
    for row in range(rowCount):
        value = dataTable.getFloat(row, 1)
        if value > dataMax:
            dataMax = value
        if value < dataMin:
            dataMin = value
   
def draw():
    global locationTable
    global mapImage
    global rowCount

    global dataTable
    global dataMin
    global dataMax
    
    background(255)
    
    #print(rowCount)
    image(mapImage, 0, 0)
    fill(192, 0, 0)
    noStroke()
    
    for row in range(0,rowCount):
        abbrev = dataTable.getRowName(row)
        x = locationTable.getFloat2(abbrev, 1)
        y = locationTable.getFloat2(abbrev, 2)
        drawData(x, y, abbrev)
        
# Map the size of the ellipse to the data value
def drawData(x, y, abbrev):
    global dataTable
    global dataMin
    global dataMax

    #Get data value for state
    value = dataTable.getFloat2(abbrev, 1)
    #Re-map the value to a number between 2 and 40
    mapped = map(value, dataMin, dataMax, 2, 40)
    #Draw an ellipse for this item
    ellipse(x, y, mapped, mapped)

import Table

dataMin = 0

dataMax = 0

def setup():

global locationTable

global mapImage

global rowCount

global dataTable

global dataMin

global dataMax

size(640, 400)

mapImage = loadImage("map.png")

locationTable = Table.Table("locations.tsv")

rowCount = locationTable.getRowCount()

dataTable = Table.Table("random.tsv")

# Find the minimum and maximum values

for row in range(rowCount):

value = dataTable.getFloat(row, 1)

if value > dataMax:

dataMax = value

if value < dataMin:

dataMin = value

def draw():

global locationTable

global mapImage

global rowCount

global dataTable

global dataMin

global dataMax

background(255)

#print(rowCount)

image(mapImage, 0, 0)

fill(192, 0, 0)

noStroke()

for row in range(0,rowCount):

abbrev = dataTable.getRowName(row)

x = locationTable.getFloat2(abbrev, 1)

y = locationTable.getFloat2(abbrev, 2)

drawData(x, y, abbrev)

# Map the size of the ellipse to the data value

def drawData(x, y, abbrev):

global dataTable

global dataMin

global dataMax

#Get data value for state

value = dataTable.getFloat2(abbrev, 1)

#Re-map the value to a number between 2 and 40

mapped = map(value, dataMin, dataMax, 2, 40)

#Draw an ellipse for this item

ellipse(x, y, mapped, mapped)

Output:

Science To Medicine

Just My Daily Study Note by ts.anesth.kpum